To control the inorganic nitrogen and biofloc concentrations in the biofloc system, it is necessary to intensify the nitrogen removal by nitrification and denitrification. In this study, nitrifiers and aerobic denitrifying bacteria were inoculated into aquaculture wastewater, with 16.80 mg/L of nitrogen input per day after start‐up, and by addition of glucose and citrate C/N to 9 and 12, without adding carbon source as control (C/N 6.17). The concentrations of inorganic nitrogen, total nitrogen and biofloc, and the diversity of the microbial community were investigated during the experimental period of 40 days. The results showed that 84.17–89.97% of nitrogen input was removed in all the treatments, residual nitrogen was higher in the glucose treatments. Lower inorganic nitrogen at a higher C/N ratio was obtained with the addition of the same carbon source due to more assimilation. Among all, the citrate treatment at C/N 12 obtained the best control in inorganic nitrogen concentrations and better in biofloc concentration owing to efficient dissimilation and assimilation. Moreover, from day 26 to day 40, the number of detected OTUs increased by 22.90–58.40% while the Shannon indices have not changed much in all the treatments. Ten of the top 15 genera were the typical denitrifying genera in each treatment, the total abundance of these decreased by 7.00% to 58.00% while that of Paracoccus, as one of the denitrifiers added, increased by 3.00% to 25.00%. This suggested that the addition of citrate at higher C/N could improve the denitrification function of biofloc system.